<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">You need to make sure the same version of MPI is used to compile and run MAKER. When installing MAKER make sure the mpi.h and mpicc indicated during configuration come from the same version of OpenMPI as the mpiexec command you are using now.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div><font face="Calibri,sans-serif">Also for OpenMPI run the following command before setting up or launching MAKER --></font></div><div><font face="Calibri,sans-serif"><span class="Apple-tab-span" style="white-space:pre"> </span>export LD_PRELOAD=/openmpi_location/lib/libmpi.so</font></div><div><br></div><div><font face="Calibri,sans-serif">replace openmpi_location in the above command with the location of your OpenMPI.</font></div><div><font face="Calibri,sans-serif"><br></font></div><div>Setting <font face="Calibri,sans-serif">LD_PRELOAD preload is required for OpenMPI to work correctly with shared libraries.</font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">Also you may need to add the following to your MPI command before running MAKER.</font></div><div><font face="Calibri,sans-serif">--> -mca btl ^openib</font></div><div><font face="Calibri,sans-serif">Example --> mpiexec -mca btl ^openib -n 40 maker </font></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> rens holmer <<a href="mailto:rens.holmer@wur.nl">rens.holmer@wur.nl</a>><br><span style="font-weight:bold">Date: </span> Tuesday, August 19, 2014 at 3:19 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker error mpiexec<br></div><div><br></div><div dir="ltr">Hi,<div><br></div><div>I am trying to run maker using MPI, and I get an error I do not understand.</div><div><br></div><div>Maker version: 2.13.6</div><div>mpiexec version: mpiexec (OpenRTE) 1.6.5</div><div><br></div><div>When I run ./Build status it is reported that MPI is enabled.</div><div><br></div><div>When I run mpiexec -n 40 maker I get the following errors:</div><div><br></div><div><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25563] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">[assembly:25562] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)</p><p class="">--------------------------------------------------------------------------</p><p class="">It looks like opal_init failed for some reason; your parallel process is</p><p class="">likely to abort. There are many reasons that a parallel process can</p><p class="">fail during opal_init; some of which are due to configuration or</p><p class="">environment problems. This failure appears to be an internal failure;</p><p class="">here's some additional information (which may only be relevant to an</p><p class="">Open MPI developer):</p><p class=""><br></p><p class=""> opal_shmem_base_select failed</p><p class=""> --> Returned value -1 instead of OPAL_SUCCESS</p><p class="">--------------------------------------------------------------------------</p><p class="">--------------------------------------------------------------------------</p><p class=""><br></p><p class=""><br></p><p class="">Etcetera etcetera.</p><p class="">However: when I search for the files reported as missing I do find them, and I don't believe they are from a different version of MPI?<br><br>Am I using a wrong version of MPI?<br><br>Any help would be appreciated,</p><p class="">Sincerely,</p><p class=""><br></p><p class="">Rens Holmer</p></div><div><br></div></div>
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